I've never taken the ferry, but if you're going over Chuseok, I'd look at booking your ticket asap. You might also want to check out AirBusan, as it might be a similar price to the ferry. They have an English website.
I've been to Nagasaki a few times - it's a nice little city. If you take a limited express train, it's about 2 hours from Fukuoka.
You also might want to check out Kumamoto, as it's got one of the best castles in Japan. You could sleep in Fukuoka and just do day trips to each city. Check out the Northern Kyushu 3 day Rail Pass for 7,000 yen: